def work_helper_image_files():
'''Test the static methods in scan_helper_image_files.'''
helper = scan_helper_image_files()
import dxtbx
directory = os.path.join(os.path.split(dxtbx.__file__)[0], 'tests')
template = 'image_###.dat'
assert(len(scan_helper_image_files.template_directory_to_indices(
template, directory)) == 20)
assert(scan_helper_image_files.template_directory_index_to_image(
template, directory, 1) == os.path.join(directory, 'image_001.dat'))
assert(scan_helper_image_files.template_index_to_image(
template, 1) == 'image_001.dat')
assert(scan_helper_image_files.image_to_template_directory(
os.path.join(directory, 'image_001.dat')) == (template, directory))
assert(scan_helper_image_files.image_to_index('image_001.dat') == 1)
assert(scan_helper_image_files.image_to_template(
'image_001.dat') == 'image_###.dat')
assert(scan_helper_image_files.image_to_index("image_6.8kev_1_001.cbf") == 1)
return
def test_helper_image_files():
"""Test the static methods in scan_helper_image_files."""
helper = scan_helper_image_files()
import dxtbx
directory = os.path.join(os.path.split(dxtbx.__file__)[0], "tests")
template = "image_###.dat"
assert (len(
scan_helper_image_files.template_directory_to_indices(
template, directory)) == 20)
assert scan_helper_image_files.template_directory_index_to_image(
template, directory, 1) == os.path.join(directory, "image_001.dat")
assert (scan_helper_image_files.template_index_to_image(
template, 1) == "image_001.dat")
assert scan_helper_image_files.image_to_template_directory(
os.path.join(directory, "image_001.dat")) == (template, directory)
assert scan_helper_image_files.image_to_index("image_001.dat") == 1
assert scan_helper_image_files.image_to_template(
"image_001.dat") == "image_###.dat"
assert scan_helper_image_files.image_to_index(
"image_6.8kev_1_001.cbf") == 1
def test_helper_image_files(image_test_dir):
"""Test the static methods in scan_helper_image_files."""
assert scan_helper_image_files()
template = "image_###.dat"
assert (
len(
scan_helper_image_files.template_directory_to_indices(
template, image_test_dir
)
)
== 20
)
assert scan_helper_image_files.template_directory_index_to_image(
template, image_test_dir, 1
) == os.path.join(image_test_dir, "image_001.dat")
assert (
scan_helper_image_files.template_index_to_image(template, 1) == "image_001.dat"
)
assert scan_helper_image_files.image_to_template_directory(
os.path.join(image_test_dir, "image_001.dat")
) == (template, image_test_dir)
assert scan_helper_image_files.image_to_index("image_001.dat") == 1
assert scan_helper_image_files.image_to_template("image_001.dat") == "image_###.dat"
assert scan_helper_image_files.image_to_index("image_6.8kev_1_001.cbf") == 1
def work_helper_image_files():
'''Test the static methods in scan_helper_image_files.'''
helper = scan_helper_image_files()
import dxtbx
directory = os.path.join(os.path.split(dxtbx.__file__)[0], 'tests')
template = 'image_###.dat'
assert(len(scan_helper_image_files.template_directory_to_indices(
template, directory)) == 20)
assert(scan_helper_image_files.template_directory_index_to_image(
template, directory, 1) == os.path.join(directory, 'image_001.dat'))
assert(scan_helper_image_files.template_index_to_image(
template, 1) == 'image_001.dat')
assert(scan_helper_image_files.image_to_template_directory(
os.path.join(directory, 'image_001.dat')) == (template, directory))
assert(scan_helper_image_files.image_to_index('image_001.dat') == 1)
assert(scan_helper_image_files.image_to_template(
'image_001.dat') == 'image_###.dat')
assert(scan_helper_image_files.image_to_index("image_6.8kev_1_001.cbf") == 1)
return
def imgCIF_H(cif_file, cbf_handle):
"""Initialize a scan model from an imgCIF file handle, where it is
assumed that the file has already been read."""
exposure = cbf_handle.get_integration_time()
timestamp = cbf_handle.get_timestamp()[0]
gonio = cbf_handle.construct_goniometer()
try:
angles = tuple(gonio.get_rotation_range())
except Exception as e:
if str(e).strip() == "CBFlib Error(s): CBF_NOTFOUND":
# probaby a still shot -> no scan object
return None
raise
# xia2-56 handle gracefully reverse turning goniometers - this assumes the
# rotation axis is correctly inverted in the goniometer factory
if angles[1] < 0:
angles = -angles[0], -angles[1]
index = scan_helper_image_files.image_to_index(cif_file)
gonio.__swig_destroy__(gonio)
return ScanFactory.make_scan((index, index), exposure, angles,
{index: timestamp})
def single_file(filename, exposure_times, osc_start, osc_width, epoch):
"""Construct an scan instance for a single image."""
index = scan_helper_image_files.image_to_index(
os.path.split(filename)[-1])
if epoch is None:
epoch = 0.0
return ScanFactory.make_scan((index, index), exposure_times,
(osc_start, osc_width), {index: epoch})
def single_file(filename, exposure_times, osc_start, osc_width, epoch):
"""Construct an scan instance for a single image."""
index = scan_helper_image_files.image_to_index(
os.path.split(filename)[-1])
if epoch is None:
epoch = 0.0
# if the oscillation width is negative at this stage it is almost
# certainly an artefact of the omega end being 0 when the omega start
# angle was ~ 360 so it would be ~ -360 - see dxtbx#378
if osc_width < -180:
osc_width += 360
return ScanFactory.make_scan((index, index), exposure_times,
(osc_start, osc_width), {index: epoch})
class ScanFactory:
'''A factory for scan instances, to help with constructing the classes
in a set of common circumstances.'''
@staticmethod
def from_phil(params, reference=None):
'''
Generate a scan model from phil parameters
'''
if reference is None:
if params.scan.image_range is None and params.scan.oscillation is None:
return None
if params.scan.image_range is None:
raise RuntimeError('No image range set')
if params.scan.oscillation is None:
raise RuntimeError('No oscillation set')
scan = Scan(
params.scan.image_range,
params.scan.oscillation)
else:
scan = reference
if params.scan.image_range is not None:
most_recent_image_index = scan.get_image_range()[1] - scan.get_image_range()[0]
scan.set_oscillation(
scan.get_image_oscillation(
params.scan.image_range[0]))
scan.set_image_range(params.scan.image_range)
if params.scan.extrapolate_scan and \
(params.scan.image_range[1] - params.scan.image_range[0]) > most_recent_image_index:
exposure_times = scan.get_exposure_times()
epochs = scan.get_epochs()
exposure_time = exposure_times[most_recent_image_index]
epoch_correction = epochs[most_recent_image_index]
for i in range(most_recent_image_index + 1, \
params.scan.image_range[1] - params.scan.image_range[0] + 1):
exposure_times[i] = exposure_time
epoch_correction += exposure_time
epochs[i] = epoch_correction
scan.set_epochs(epochs)
scan.set_exposure_times(exposure_times)
if params.scan.oscillation is not None:
scan.set_oscillation(params.scan.oscillation)
# Return the model
return scan
@staticmethod
def from_dict(d, t=None):
''' Convert the dictionary to a scan model
Params:
d The dictionary of parameters
t The template dictionary to use
Returns:
The scan model
'''
from dxtbx.model import Scan
from scitbx.array_family import flex # import dependency
# If None, return None
if d == None:
if t == None: return None
else: return from_dict(t, None)
elif t != None:
d = dict(t.items() + d.items())
if not isinstance(d['exposure_time'], list):
d['exposure_time'] = [d['exposure_time']]
# Create the model from the dictionary
return Scan.from_dict(d)
@staticmethod
def make_scan(image_range, exposure_times, oscillation, epochs, deg=True):
from scitbx.array_family import flex
if not isinstance(exposure_times, list):
num_images = image_range[1] - image_range[0] + 1
exposure_times = [exposure_times for i in range(num_images)]
else:
num_images = image_range[1] - image_range[0] + 1
num_exp = len(exposure_times)
if num_exp != num_images:
if (num_exp == 0):
exposure_times = [0 for i in range(num_images)]
else:
exposure_times = exposure_times.extend(
[exposure_times[-1] for i in range(num_images - num_exp)])
epoch_list = [epochs[j] for j in sorted(epochs)]
return Scan(
tuple(map(int, image_range)),
tuple(map(float, oscillation)),
flex.double(list(map(float, exposure_times))),
flex.double(list(map(float, epoch_list))),
deg)
@staticmethod
def single(filename, format, exposure_times, osc_start, osc_width, epoch):
'''Construct an scan instance for a single image.'''
import os
index = scan_helper_image_files.image_to_index(os.path.split(filename)[-1])
if epoch is None:
epoch = 0.0
return ScanFactory.make_scan(
(index, index), exposure_times, (osc_start, osc_width),
{index:epoch})
@staticmethod
def imgCIF(cif_file):
'''Initialize a scan model from an imgCIF file.'''
cbf_handle = pycbf.cbf_handle_struct()
cbf_handle.read_file(cif_file, pycbf.MSG_DIGEST)
return ScanFactory.imgCIF_H(cif_file, cbf_handle)
@staticmethod
def imgCIF_H(cif_file, cbf_handle):
'''Initialize a scan model from an imgCIF file handle, where it is
assumed that the file has already been read.'''
exposure = cbf_handle.get_integration_time()
timestamp = cbf_handle.get_timestamp()[0]
gonio = cbf_handle.construct_goniometer()
try:
angles = tuple(gonio.get_rotation_range())
except Exception, e:
if str(e).strip() == 'CBFlib Error(s): CBF_NOTFOUND':
# probaby a still shot -> no scan object
return None
raise
# xia2-56 handle gracefully reverse turning goniometers - this assumes the
# rotation axis is correctly inverted in the goniometer factory
if angles[1] < 0:
angles = -angles[0], -angles[1]
index = scan_helper_image_files.image_to_index(cif_file)
gonio.__swig_destroy__(gonio)
return ScanFactory.make_scan(
(index, index), exposure, angles, {index:timestamp})
